Merge pull request #1 from stulacy/bugfix/markdown-dependency

Bugfix/markdown dependency

DESCRIPTION

@@ -1,15 +1,15 @@
 Package: rprev
 Type: Package
 Title: Estimating Disease Prevalence from Registry Data
-Version: 1.0.4
-Date: 2020-03-19
+Version: 1.0.5
+Date: 2021-04-30
 Authors@R: c(
         person("Stuart", "Lacy", email="stuart.lacy@york.ac.uk", role=c('cre', 'aut')),
         person("Simon", "Crouch", email="simon.crouch@york.ac.uk", role='aut'),
         person("Stephanie", "Lax", email="stephanie.lax@york.ac.uk", role='aut')
         )
-Description: Estimates disease prevalence for a given index date, using existing
-    registry data extended with Monte Carlo simulations.
+Description: Estimates disease prevalence for a given index date using existing
+    registry data extended with Monte Carlo simulations following the method of Crouch et al (2014) <doi: 10.1016/j.canep.2014.02.005>.
 LazyData: true
 License: GPL-2
 Depends:
@@ -23,11 +23,12 @@ Imports:
     lubridate,
     magrittr,
     tidyr
-RoxygenNote: 7.1.0
+RoxygenNote: 7.1.1
 Suggests:
     flexsurv,
     flexsurvcure,
     knitr,
+    rmarkdown,
     rms,
     testthat,
     covr

R/data.R

@@ -2,7 +2,7 @@
 #'
 #' A dataset containing daily population survival rates for individuals up to 100 years old,
 #' from the UK population, derived from the 2009 mortality rates found at:
-#' \url{http://www.ons.gov.uk/ons/taxonomy/index.html?nscl=Life+Tables#tab-data-tables},
+#' \url{https://www.ons.gov.uk/peoplepopulationandcommunity/birthsdeathsandmarriages/lifeexpectancies/datasets/nationallifetablesunitedkingdomreferencetables},
 #' Adapted from public sector information licensed under the Open Government Licence v3.0.
 #' Data were relabelled according to the mean year of the three-year birth window.
 #' It is stored as a \code{data.table} for efficient access.

README.md

@@ -11,7 +11,7 @@ Monte Carlo simulation techniques are used to simulate incident cases in years f
 
 Prevalence arises from two independent stochastic processes: disease incidence and survival.
 Default models are provided that model incidence as a homogeneous Poisson process and survival as a standard parameteric distribution, although both of these models can be user specified for further control.
-See the *user_guide* vignette for more details about the implementation, and the original publication for details of the algorithm, available at [http://www.ncbi.nlm.nih.gov/pubmed/24656754](http://www.ncbi.nlm.nih.gov/pubmed/24656754).
+See the *user_guide* vignette for more details about the implementation, and the original publication for details of the algorithm, available at [https://pubmed.ncbi.nlm.nih.gov/24656754/](https://pubmed.ncbi.nlm.nih.gov/24656754/).
 
 ## Installation
 

cran-comments.md

@@ -1,16 +1,24 @@
+## Resubmission 2
+
+Updated URL with https that had missed out in previous submission.
+
+## Resubmission
+
+Updated URLs with https and corrected out-of-date links. 
+Added DOI to package description.
+
 ## Release summary
 
-Made changes to account for the upcoming stringsAsFactors = FALSE default argument to data.frame() in R 4.0 so that the package is backwards compatible.
+Explicitly declared `rmarkdown` dependency in SUGGESTS for building the vignette.
 
 ## Test environments
 
-* local Manjaro Linux install, R 3.6.3
-* Win-builder R 3.6.3
+* local Manjaro Linux install, R 4.0.5
 * Win-builder r-devel
 
 ## R CMD check results
 
-There were no ERRORS, WARNINGS, or NOTES.
+There were no ERRORS or WARNINGS, and the only NOTE refers to possible mis-spelling of the words 'et' and 'al' in the DESCRIPTION.
 
 ## Downstream dependencies
 

vignettes/bibliography.bib

@@ -7,7 +7,7 @@ @article{crouch2014determining
   pages={193--199},
   year={2014},
   publisher={Elsevier},
-  url={http://www.ncbi.nlm.nih.gov/pubmed/24656754}
+  url={https://pubmed.ncbi.nlm.nih.gov/24656754/}
 }
 
 @misc{ons,